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- PDB-7boa: A hexameric de novo coiled-coil assembly: CC-Type2-(YaFd)4-W19(BrPhe). -

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Basic information

Entry
Database: PDB / ID: 7boa
TitleA hexameric de novo coiled-coil assembly: CC-Type2-(YaFd)4-W19(BrPhe).
ComponentsCC-Type2-(YaFd)4-W19(BrPhe)
KeywordsDE NOVO PROTEIN / Coiled coil / synthetic peptide / homomeric assembly / tyrosine-tyrosine interactions
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsRhys, G.G. / Martin, F.J.O. / Brady, R.L. / Woolfson, D.N.
Funding supportEuropean Union, United Kingdom, 2items
OrganizationGrant numberCountry
European Research Council (ERC)340764European Union
Engineering and Physical Sciences Research CouncilEP/G036764/1 United Kingdom
CitationJournal: Biomacromolecules / Year: 2021
Title: How Coiled-Coil Assemblies Accommodate Multiple Aromatic Residues.
Authors: Rhys, G.G. / Dawson, W.M. / Beesley, J.L. / Martin, F.J.O. / Brady, R.L. / Thomson, A.R. / Woolfson, D.N.
History
DepositionJan 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CC-Type2-(YaFd)4-W19(BrPhe)
B: CC-Type2-(YaFd)4-W19(BrPhe)
C: CC-Type2-(YaFd)4-W19(BrPhe)
D: CC-Type2-(YaFd)4-W19(BrPhe)
E: CC-Type2-(YaFd)4-W19(BrPhe)
F: CC-Type2-(YaFd)4-W19(BrPhe)
G: CC-Type2-(YaFd)4-W19(BrPhe)
H: CC-Type2-(YaFd)4-W19(BrPhe)


Theoretical massNumber of molelcules
Total (without water)28,8878
Polymers28,8878
Non-polymers00
Water5,459303
1
A: CC-Type2-(YaFd)4-W19(BrPhe)
B: CC-Type2-(YaFd)4-W19(BrPhe)
C: CC-Type2-(YaFd)4-W19(BrPhe)
D: CC-Type2-(YaFd)4-W19(BrPhe)


Theoretical massNumber of molelcules
Total (without water)14,4434
Polymers14,4434
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: CC-Type2-(YaFd)4-W19(BrPhe)
F: CC-Type2-(YaFd)4-W19(BrPhe)
G: CC-Type2-(YaFd)4-W19(BrPhe)
H: CC-Type2-(YaFd)4-W19(BrPhe)


Theoretical massNumber of molelcules
Total (without water)14,4434
Polymers14,4434
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.707, 75.608, 88.123
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21H
12B
22H
13C
23H
14D
24H
15E
25H
16F
26H
17G
27H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A2 - 30
2010H2 - 30
1020B2 - 30
2020H2 - 30
1030C2 - 30
2030H2 - 30
1040D2 - 30
2040H2 - 30
1050E2 - 30
2050H2 - 30
1060F2 - 30
2060H2 - 30
1070G2 - 30
2070H2 - 30

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

#1: Protein/peptide
CC-Type2-(YaFd)4-W19(BrPhe)


Mass: 3610.858 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: After 1:1 dilution with the peptide solution, the resulting conditions were 0.1 M Ammonium sulphate, 0.05 M Sodium acetate and 5% w/v PEG 2000 monomethyl ether.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.91991 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91991 Å / Relative weight: 1
ReflectionResolution: 1.65→75.57 Å / Num. obs: 33544 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 22.97 Å2 / CC1/2: 1 / CC star: 0.999 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.036 / Rrim(I) all: 0.13 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible allCC star
7.38-75.5711.10.04821.545710.0150.0599.9
1.65-1.6913.61.9681.124420.7920.5482.041000.952

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
xia20.5.898-g5f4e2fb3-dials-1.14data scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
DIALS1.14.9-g0c59d74b8-releasedata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→57.45 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.393 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1710 5.1 %RANDOM
Rwork0.2208 ---
obs0.2224 31729 99.82 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 146.75 Å2 / Biso mean: 34.793 Å2 / Biso min: 19.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2--2.27 Å20 Å2
3----3.37 Å2
Refinement stepCycle: final / Resolution: 1.65→57.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 0 303 2335
Biso mean---43.15 -
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132176
X-RAY DIFFRACTIONr_bond_other_d0.0030.0181887
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.6792858
X-RAY DIFFRACTIONr_angle_other_deg11.5141.5934374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.4255232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04223.583127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04815336
X-RAY DIFFRACTIONr_chiral_restr0.070.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022465
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02559
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A27150.17
12H27150.17
21B28270.12
22H28270.12
31C27280.15
32H27280.15
41D29190.09
42H29190.09
51E28900.11
52H28900.11
61F28370.12
62H28370.12
71G28210.12
72H28210.12
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 142 -
Rwork0.381 2270 -
all-2412 -
obs--99.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.06410.20342.18921.20850.284912.9355-0.03710.02370.0667-0.0476-0.04080.0772-0.3167-0.61940.07790.0360.03290.0020.0528-0.00780.031215.44513.67565.713
21.7630.08841.63532.21320.708311.93240.06520.049-0.0919-0.21010.00230.18330.4272-0.6648-0.06750.0539-0.0366-0.01840.0601-0.0180.083914.8422.13463.082
31.5108-0.50070.74312.5836-0.702614.5864-0.02910.0284-0.0756-0.0673-0.0317-0.04640.56930.55510.06080.04460.0311-0.01170.03130.01150.086824.4941.92464.844
42.661-0.68812.5661.9632-0.468913.38640.02850.18010.0014-0.1949-0.0552-0.1361-0.38420.6220.02670.0475-0.01720.0160.03230.00460.035624.30713.38161.995
52.22880.28191.32794.2808-1.503314.945-0.37870.07930.3530.20520.0859-0.1772-0.66990.66070.29280.0882-0.0255-0.07260.03620.00240.09335.084-6.16765.059
62.27910.20352.50053.3071-3.364417.2322-0.22550.1592-0.01760.01340.2345-0.19580.41510.3879-0.0090.070.018-0.00720.0473-0.01470.04935.102-15.23562.174
71.7918-0.41830.49472.12411.359513.4305-0.1967-0.1889-0.06590.19130.04870.11860.4854-0.48790.14790.05220.00130.02670.04050.00220.0595-6.16-15.39565.695
82.49640.55051.95713.19892.111416.2655-0.3604-0.09890.25390.09880.12710.2413-0.7024-0.52340.23330.08720.0497-0.03820.0404-0.01610.1015-6.573-6.20763.092
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 30
2X-RAY DIFFRACTION2B1 - 30
3X-RAY DIFFRACTION3C1 - 30
4X-RAY DIFFRACTION4D1 - 30
5X-RAY DIFFRACTION5E1 - 30
6X-RAY DIFFRACTION6F1 - 30
7X-RAY DIFFRACTION7G1 - 30
8X-RAY DIFFRACTION8H1 - 30

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